全基因组关联分析在玉米籽粒性状研究中的应用及其候选基因预测

doi:10.11923/j.issn.2095-4050.cjas2023-0092

农学学报 ›› 2024, Vol. 14 ›› Issue (4): 26-36.doi: 10.11923/j.issn.2095-4050.cjas2023-0092

全基因组关联分析在玉米籽粒性状研究中的应用及其候选基因预测

陈昕怡(), 刘晨艳, 华明珠, 徐欣, 冯汶祥, 汪保华, 方辉()

南通大学生命科学学院，江苏南通 226019

收稿日期:2023-04-03 修回日期:2023-09-15 出版日期:2024-04-17 发布日期:2024-04-17
通讯作者:
方辉，男，1989年出生，山东威海人，讲师，博士，主要从事玉米功能基因组学研究。通信地址：226019 江苏省南通市崇川区啬园路9号南通大学主校区纺化楼C1114，E-mail：fanghui8912@126.com。
作者简介:
陈昕怡，女，2003年出生，江苏苏州人，本科，研究方向：玉米数量性状的遗传解析。通信地址：226019 江苏省南通市崇川区啬园路9号南通大学主校区，E-mail：583057819@qq.com。
基金资助:
国家自然科学基金项目“玉米籽粒油份基因ZmCtBP1的分子遗传机制研究”(32101730); 南通大学大学生创新训练计划项目“玉米籽粒发育基因ZmPPR6的克隆及功能分析”(2022098)

Grain-related Traits in Maize: Genome-wide Association Analysis and Candidate Gene Prediction

CHEN Xinyi(), LIU Chenyan, HUA Mingzhu, XU Xin, FENG Wenxiang, WANG Baohua, FANG Hui()

School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China

Received:2023-04-03 Revised:2023-09-15 Online:2024-04-17 Published:2024-04-17

摘要/Abstract

摘要：

本研究旨在探索调控玉米籽粒发育的自然变异，以期为玉米产量性状的遗传改良提供科学依据。以150份遗传变异丰富的玉米自交系为材料进行研究。通过结合34342个SNP标记和3种模型，对5个籽粒相关性状进行全基因组关联分析。研究结果揭示了18个独立位点与目标性状显著关联，每个位点能够解释12.24%~15.41%的表型变异。同时，研究发现4对与籽粒长度相关的SNP之间存在显著的上位性互作，这些互作共能解释5.32%的表型变异。为了深入理解这些关联位点背后的分子机制，结合B73自交系籽粒发育的动态转录组数据和基因的功能注释，预测了19个候选基因，这些候选基因可以分为4类：6个酶、3个核糖体蛋白、1个转录因子和9个其他蛋白。这些候选基因的发现为解析玉米籽粒发育的分子机制以及改良籽粒大小和作物产量提供新的基因资源。通过本研究，我们不仅揭示了调控玉米籽粒发育的自然变异，还为玉米产量性状的遗传改良提供了新的基因资源。这些成果有望为玉米育种工作带来新的突破，提高玉米产量，从而更好地满足人类对粮食的需求。

关键词: 玉米, 籽粒大小, 产量, 全基因组关联分析, 候选基因预测

Abstract:

To explore the natural variations in regulating the maize kernel development and to assist in the genetic improvement of maize yield traits, in this study, 150 maize inbred lines with rich genetic variations were selected as materials for investigation. Combining 34,342 SNP markers and three models, a genome-wide association analysis was conducted on five grain-related traits. The results revealed that a total of 18 independent loci were significantly associated with the target traits, with each locus accounting for 12.24% to 15.41% of the phenotypic variations. Additionally, significant epistatic interactions were identified among four pairs of SNPs associated with kernel length, collectively explaining 5.32% of the phenotypic variations. By integrating the dynamic transcriptome data of kernel development in the B73 inbred line and functional annotations of genes, 19 candidate genes were predicted and classified into four categories: 6 enzymes, 3 ribosomal proteins, 1 transcription factor, and 9 other proteins. These candidate genes provide new genetic resources for deciphering the molecular mechanisms of maize kernel development and enhancing maize kernel size and yield. Through this research, we have not only uncovered the natural variations that regulate the development of corn kernels but also provided new genetic resources for the genetic improvement of corn yield traits. These findings are expected to bring new breakthroughs in corn breeding efforts, enhance corn production, and thereby better meet human needs for food.

Key words: maize, kernel size, yield, genome-wide association analysis, candidate genes prediction

陈昕怡, 刘晨艳, 华明珠, 徐欣, 冯汶祥, 汪保华, 方辉. 全基因组关联分析在玉米籽粒性状研究中的应用及其候选基因预测[J]. 农学学报, 2024, 14(4): 26-36.

CHEN Xinyi, LIU Chenyan, HUA Mingzhu, XU Xin, FENG Wenxiang, WANG Baohua, FANG Hui. Grain-related Traits in Maize: Genome-wide Association Analysis and Candidate Gene Prediction[J]. Journal of Agriculture, 2024, 14(4): 26-36.

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性状	自交系个数	最小值	最大值	平均值±标准差	变异系数	广义遗传力	置信区间
HKW/g	150	8.28	31.07	20.49 ± 4.12	20.11	0.995	0.994~0.997
KL/mm	150	7.37	10.00	8.75 ± 0.51	5.83	0.653	0.530~0.744
KW/mm	150	6.82	9.08	8.17 ± 0.37	4.53	0.916	0.886~0.938
KT/mm	150	3.97	6.12	4.79 ± 0.41	8.56	0.849	0.795~0.888
KV/mL	150	0.10	0.26	0.17 ± 0.03	17.65	0.523	0.354~0.647

性状	自交系个数	最小值	最大值	平均值±标准差	变异系数	广义遗传力	置信区间
HKW/g	150	8.28	31.07	20.49 ± 4.12	20.11	0.995	0.994~0.997
KL/mm	150	7.37	10.00	8.75 ± 0.51	5.83	0.653	0.530~0.744
KW/mm	150	6.82	9.08	8.17 ± 0.37	4.53	0.916	0.886~0.938
KT/mm	150	3.97	6.12	4.79 ± 0.41	8.56	0.849	0.795~0.888
KV/mL	150	0.10	0.26	0.17 ± 0.03	17.65	0.523	0.354~0.647

	HKW	KL	KW	KT	KV
HKW	1	4.62E-16	5.70E-16	3.25E-11	3.32E-31
KL	0.65	1	3.34E-05	2.05E-01	4.87E-12
KW	0.65	0.36	1	3.42E-02	1.03E-09
KT	0.55	0.12	0.19	1	2.23E-09
KV	0.82	0.57	0.52	0.51	1

	HKW	KL	KW	KT	KV
HKW	1	4.62E-16	5.70E-16	3.25E-11	3.32E-31
KL	0.65	1	3.34E-05	2.05E-01	4.87E-12
KW	0.65	0.36	1	3.42E-02	1.03E-09
KT	0.55	0.12	0.19	1	2.23E-09
KV	0.82	0.57	0.52	0.51	1

性状	标记	染色体	物理位置	P值	R²/%	候选基因_V3	候选基因_V4	功能注释	备注
KL	PUT-163a-4730462-2143	1	49131053	7.94E-05	12.51	GRMZM2G038015	Zm00001d028879	bZIP-transcription factor 24
KL	PZE-101070408	1	53158367	5.13E-05	13.56	GRMZM2G107463	Zm00001d028989	RING/U-box superfamily protein
HKW	SYN29761	1	90219767	2.75E-05	14.29	GRMZM2G154487	Zm00001d029887	Ribosomal L18p/L5e family protein
KV	PZE-102077877	2	60656421	5.47E-05	13.80	GRMZM2G016749	Zm00001d000124	Protein-serine/threonine phosphatase
KW	PZE-103124207	3	181695567	1.10E-05	15.41	GRMZM2G386991	Zm00001d042938	Serine/threonine-protein kinase AFC1
KL	ZM013522-0530	3	222667473	1.22E-05	15.26	GRMZM5G866024	Zm00001d044376	membrane protein
KT	SYNGENTA2236	4	5010855	8.07E-05	12.86	GRMZM2G101502	Zm00001d018506	Deoxyhypusine hydroxylase	条件分析
KL	SYN3700	5	216163416	1.93E-05	14.62	GRMZM2G101571	Zm00001d018507	bet1 sft1-related snare
KL	PZE-106060527	6	109295972	1.13E-05	15.25	GRMZM2G048194	Zm00001d037151	erwinia induced protein 1
KV	PZE-106082684	6	139912054	9.34E-05	12.71	GRMZM2G068496	Zm00001d037972	60S ribosomal protein L29	条件分析
KV	PZE-106082684	6	139912054	9.34E-05	12.71	GRMZM2G068323	Zm00001d037975	pentatricopeptide repeat-containing protein	条件分析
HKW	SYN38610	6	165943896	7.25E-05	12.74	GRMZM2G132929	Zm00001d039106	40S ribosomal protein S12-like
HKW	PZE-108019862	8	17889483	8.97E-05	12.47	GRMZM2G080722	Zm00001d008736	Monothiol glutaredoxin-S4, mitochondrial
KT	PZE-108040469	8	65972918	1.05E-05	15.35	GRMZM2G021331	Zm00001d009488	ATP synthase beta chain
KL	PZE-108113799	8	164939218	7.41E-05	14.74	GRMZM2G049269	Zm00001d012211	ankyrin-like protein
KL	PZE-109030021	9	33672066	7.05E-05	12.78	GRMZM2G065355	Zm00001d045724	heat shock factor-binding protein 1
KL	SYN32340	9	90842290	6.11E-05	13.20	GRMZM2G056166	Zm00001d046531	bri1-kd interacting protein 118
KL	PZE-109077339	9	124770857	2.27E-05	14.39	GRMZM2G113866	Zm00001d047335	sigma factor sigB regulation protein rsbQ
KL	PZE-110109454	10	148515533	9.38E-05	12.24	GRMZM2G173636	Zm00001d026639	acyl-binding domain-containing protein 6

全基因组关联分析在玉米籽粒性状研究中的应用及其候选基因预测

Grain-related Traits in Maize: Genome-wide Association Analysis and Candidate Gene Prediction

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性状	SNP1	SNP2	P值	add_R²/%^a	epi_R²/%^b
KL	PUT-163a-4730462-2143	ZM013522-0530	0.02	53.39	5.32
KL	PUT-163a-4730462-2143	PZE-109077339	0.03	53.39	5.32
KL	PZE-101070408	PZE-110109454	0.02	53.39	5.32
KL	PZE-108113799	PZE-109077339	0.01	53.39	5.32
KV	-	-	-	20.13	-
KT	-	-	-	22.63	-
HKW	-	-	-	22.79	-
KV	-	-	-	15.41	-

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